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mysqldump is dumping only the table structures, without data, by default.

mysqldump -u user -d database -p

Which is the option to dump is with data? How can I configure it, to include the data? (I guess it's possible with a setting in /etc/mysql/my.cnf)

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Use only

mysqldump -u user -p database

The -d option means no-data :

   --no-data, -d

       Do not write any table row information (that is, do not dump table contents). This is useful if you want to dump only the CREATE TABLE
       statement for the table (for example, to create an empty copy of the table by loading the dump file).

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